Reconstruction of Ribosomal RNA Genes from Metagenomic Data

Fan, Lu, McElroy, Kerensa and Thomas, Torsten (2012) Reconstruction of Ribosomal RNA Genes from Metagenomic Data. PLoS One, 7 6: . doi:10.1371/journal.pone.0039948

Author Fan, Lu
McElroy, Kerensa
Thomas, Torsten
Title Reconstruction of Ribosomal RNA Genes from Metagenomic Data
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2012-06
Sub-type Article (original research)
DOI 10.1371/journal.pone.0039948
Open Access Status DOI
Volume 7
Issue 6
Total pages 9
Place of publication San Francisco, CA United States
Publisher Public Library of Science
Collection year 2013
Language eng
Formatted abstract
Direct sequencing of environmental DNA (metagenomics) has a great potential for describing the 16S rRNA gene diversity of microbial communities. However current approaches using this 16S rRNA gene information to describe community diversity suffer from low taxonomic resolution or chimera problems. Here we describe a new strategy that involves stringent assembly and data filtering to reconstruct full-length 16S rRNA genes from metagenomicpyrosequencing data. Simulations showed that reconstructed 16S rRNA genes provided a true picture of the community diversity, had minimal rates of chimera formation and gave taxonomic resolution down to genus level. The strategy was furthermore compared to PCRbased methods to determine the microbial diversity in two marine sponges. This showed that about 30% of the abundant phylotypes reconstructed from metagenomic data failed to be amplified by PCR. Our approach is readily applicable to existing metagenomic datasets and is expected to lead to the discovery of new microbial phylotypes.
Keyword Marine Microbial Diversity
Sequencing Data
Phylogenetic Classification
Dna Sequences
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Advanced Water Management Centre Publications
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Citation counts: TR Web of Science Citation Count  Cited 22 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 25 times in Scopus Article | Citations
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Created: Wed, 17 Apr 2013, 14:15:02 EST by Chris Fan on behalf of Advanced Water Management Centre